Merge pull request #1113 from karanphil/fix_skip_b0_check

Fixing the skip_b0_check function

scilpy/gradients/bvec_bval_tools.py

@@ -55,7 +55,8 @@ def normalize_bvecs(bvecs):
     return bvecs
 
 
-def check_b0_threshold(min_bval, b0_thr, skip_b0_check):
+def check_b0_threshold(min_bval, b0_thr, skip_b0_check,
+                       overwrite_with_min=True):
     """
     Check if the minimal bvalue is under the threshold. If not, raise an
     error to ask user to update the b0_thr.
@@ -72,6 +73,10 @@ def check_b0_threshold(min_bval, b0_thr, skip_b0_check):
     skip_b0_check: bool
         If True, and no b0 is found, only print a warning, do not raise
         an error.
+    overwrite_with_min: bool, optional
+        If True, no b0 is found, and skip_b0_check is True, the script will
+        proceed with a new b0 threshold equal to the minimal b-value. Else, the
+        script will proceed with the original b0 threshold.
 
     Returns
     -------
@@ -101,18 +106,25 @@ def check_b0_threshold(min_bval, b0_thr, skip_b0_check):
     if min_bval > b0_thr:
         if skip_b0_check:
             logging.warning(
-                'Your minimal bvalue ({}), is above the threshold ({})\n'
-                'Since --skip_b0_check was specified, the script will '
-                'proceed with a b0 threshold of {}.'
-                .format(min_bval, b0_thr, min_bval))
-            return min_bval
+                'The minimal bvalue ({}) is above the b0 threshold ({}).'
+                .format(min_bval, b0_thr))
+            if overwrite_with_min:
+                logging.warning(
+                    'Since --skip_b0_check was specified, the script will '
+                    'proceed with a b0 threshold of {}'.format(min_bval))
+                return min_bval
+            else:
+                logging.warning(
+                    'Since --skip_b0_check was specified, the script will '
+                    'proceed without b0 volumes.')
+                return b0_thr
         else:
             raise ValueError(
-                'The minimal bvalue ({}) is above the threshold ({})\n'
+                'The minimal bvalue ({}) is above the b0 threshold ({}).\n'
                 'No b0 volumes can be found.\n'
                 'Please check your data to ensure everything is correct.\n'
                 'You may also increase the threshold or use '
-                '--skip_b0_check'
+                '--skip_b0_check.'
                 .format(min_bval, b0_thr))
     return b0_thr
 

scilpy/io/btensor.py

@@ -114,7 +114,8 @@ def generate_btensor_input(in_dwis, in_bvals, in_bvecs, in_bdeltas,
             vol = nib.load(inputf)
             bvals, bvecs = read_bvals_bvecs(bvalsf, bvecsf)
             _ = check_b0_threshold(bvals.min(), b0_thr=tol,
-                                   skip_b0_check=skip_b0_check)
+                                   skip_b0_check=skip_b0_check,
+                                   overwrite_with_min=False)
             if np.sum([bvals > tol]) != 0:
                 bvals = np.round(bvals)
             if not is_normalized_bvecs(bvecs):

scilpy/io/utils.py

@@ -272,6 +272,10 @@ def add_skip_b0_check_arg(parser, will_overwrite_with_min,
         msg += ('If no b-value is found below the threshold, the script will '
                 'continue \nwith your minimal b-value as new {}.\n'
                 .format(b0_tol_name))
+    else:
+        msg += ('If no b-value is found below the threshold, the script will '
+                'continue \nwith the original {} and no b0 volumes.\n'
+                .format(b0_tol_name))
     msg += 'Use with care, and only if you understand your data.'
 
     parser.add_argument(

scripts/scil_NODDI_maps.py

@@ -116,7 +116,8 @@ def main():
     # Generate a scheme file from the bvals and bvecs files
     bvals, _ = read_bvals_bvecs(args.in_bval, args.in_bvec)
     _ = check_b0_threshold(bvals.min(), b0_thr=args.tolerance,
-                           skip_b0_check=args.skip_b0_check)
+                           skip_b0_check=args.skip_b0_check,
+                           overwrite_with_min=False)
     shells_centroids, indices_shells = identify_shells(bvals, args.tolerance,
                                                        round_centroids=True)
 

scripts/scil_dki_metrics.py

@@ -198,7 +198,8 @@ def main():
     # b0_threshold option in gradient_table probably unused, except below with
     # option dki_residual.
     _ = check_b0_threshold(bvals.min(), b0_thr=args.tolerance,
-                           skip_b0_check=args.skip_b0_check)
+                           skip_b0_check=args.skip_b0_check,
+                           overwrite_with_min=False)
     gtab = gradient_table(bvals, bvecs, b0_threshold=args.tolerance)
 
     # Processing

scripts/scil_fodf_msmt.py

@@ -158,7 +158,8 @@ def main():
     #  https://github.com/dipy/dipy/issues/3015
     # b0_threshold option in gradient_table probably unused.
     _ = check_b0_threshold(bvals.min(), b0_thr=args.tolerance,
-                           skip_b0_check=args.skip_b0_check)
+                           skip_b0_check=args.skip_b0_check,
+                           overwrite_with_min=False)
     gtab = gradient_table(bvals, bvecs, b0_threshold=args.tolerance)
 
     # Loading spheres

scripts/scil_frf_msmt.py

@@ -170,7 +170,8 @@ def main():
     # for the b0s. Using the tolerance. To fix this, we would need to change
     # the unique_bvals_tolerance and extract_dwi_shell methods.
     _ = check_b0_threshold(bvals.min(), b0_thr=args.tolerance,
-                           skip_b0_check=args.skip_b0_check)
+                           skip_b0_check=args.skip_b0_check,
+                           overwrite_with_min=False)
     list_bvals = unique_bvals_tolerance(bvals, tol=args.tolerance)
     if not np.all(list_bvals <= dti_lim):
         _, data_dti, bvals_dti, bvecs_dti = extract_dwi_shell(